PDB Short entry for 1KG8 HEADER PROTON TRANSPORT 26-NOV-01 1KG8 TITLE X-RAY STRUCTURE OF AN EARLY-M INTERMEDIATE OF BACTERIORHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARUM; SOURCE 3 ORGANISM_TAXID: 2242 KEYWDS BACTERIORHODOPSIN, INTERMEDIATE, M-STATE, PROTON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.T.FACCIOTTI,S.ROUHANI,F.T.BURKARD,F.M.BETANCOURT,K.H.DOWNING, AUTHOR 2 R.B.ROSE,G.MCDERMOTT,R.M.GLAESER REVDAT 5 16-AUG-23 1KG8 1 REMARK LINK REVDAT 4 13-JUL-11 1KG8 1 VERSN REVDAT 3 24-FEB-09 1KG8 1 VERSN REVDAT 2 24-APR-02 1KG8 1 REMARK REVDAT 1 05-DEC-01 1KG8 0 JRNL AUTH M.T.FACCIOTTI,S.ROUHANI,F.T.BURKARD,F.M.BETANCOURT, JRNL AUTH 2 K.H.DOWNING,R.B.ROSE,G.MCDERMOTT,R.M.GLAESER JRNL TITL STRUCTURE OF AN EARLY INTERMEDIATE IN THE M-STATE PHASE OF JRNL TITL 2 THE BACTERIORHODOPSIN PHOTOCYCLE. JRNL REF BIOPHYS.J. V. 81 3442 2001 JRNL REFN ISSN 0006-3495 JRNL PMID 11721006 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : THIN RESOLUTION SHELLS REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.168 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1210 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 14618 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KG8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14618 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1C8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0M NA/K PHOSPHATE, PH 5.6, MONO REMARK 280 -OLEIN CUBIC PHASE, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.12000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 54.12000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.12000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 11040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 30.37250 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 52.60671 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -30.37250 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 52.60671 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 ILE A 4 REMARK 465 PHE A 156 REMARK 465 THR A 157 REMARK 465 SER A 158 REMARK 465 LYS A 159 REMARK 465 ALA A 160 REMARK 465 GLU A 161 REMARK 465 SER A 162 REMARK 465 MET A 163 REMARK 465 ARG A 164 REMARK 465 PRO A 165 REMARK 465 GLU A 166 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 216 C14 RET A 301 1.92 REMARK 500 CE LYS A 216 C15 RET A 301 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 71 162.50 176.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 LI1 A 602 REMARK 610 LI1 A 612 REMARK 610 LI1 A 613 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI1 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI1 A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI1 A 613 DBREF 1KG8 A 1 231 UNP P02945 BACR_HALN1 13 243 SEQRES 1 A 231 GLN ALA GLN ILE THR GLY ARG PRO GLU TRP ILE TRP LEU SEQRES 2 A 231 ALA LEU GLY THR ALA LEU MET GLY LEU GLY THR LEU TYR SEQRES 3 A 231 PHE LEU VAL LYS GLY MET GLY VAL SER ASP PRO ASP ALA SEQRES 4 A 231 LYS LYS PHE TYR ALA ILE THR THR LEU VAL PRO ALA ILE SEQRES 5 A 231 ALA PHE THR MET TYR LEU SER MET LEU LEU GLY TYR GLY SEQRES 6 A 231 LEU THR MET VAL PRO PHE GLY GLY GLU GLN ASN PRO ILE SEQRES 7 A 231 TYR TRP ALA ARG TYR ALA ASP TRP LEU PHE THR THR PRO SEQRES 8 A 231 LEU LEU LEU LEU ASP LEU ALA LEU LEU VAL ASP ALA ASP SEQRES 9 A 231 GLN GLY THR ILE LEU ALA LEU VAL GLY ALA ASP GLY ILE SEQRES 10 A 231 MET ILE GLY THR GLY LEU VAL GLY ALA LEU THR LYS VAL SEQRES 11 A 231 TYR SER TYR ARG PHE VAL TRP TRP ALA ILE SER THR ALA SEQRES 12 A 231 ALA MET LEU TYR ILE LEU TYR VAL LEU PHE PHE GLY PHE SEQRES 13 A 231 THR SER LYS ALA GLU SER MET ARG PRO GLU VAL ALA SER SEQRES 14 A 231 THR PHE LYS VAL LEU ARG ASN VAL THR VAL VAL LEU TRP SEQRES 15 A 231 SER ALA TYR PRO VAL VAL TRP LEU ILE GLY SER GLU GLY SEQRES 16 A 231 ALA GLY ILE VAL PRO LEU ASN ILE GLU THR LEU LEU PHE SEQRES 17 A 231 MET VAL LEU ASP VAL SER ALA LYS VAL GLY PHE GLY LEU SEQRES 18 A 231 ILE LEU LEU ARG SER ARG ALA ILE PHE GLY HET RET A 301 20 HET LI1 A 602 6 HET LI1 A 612 18 HET LI1 A 613 13 HETNAM RET RETINAL HETNAM LI1 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14- HETNAM 2 LI1 TRIMETHYLHEXADECAN-16-YL]GLYCEROL HETSYN LI1 LIPID FRAGMENT FORMUL 2 RET C20 H28 O FORMUL 3 LI1 3(C42 H86 O3) FORMUL 6 HOH *13(H2 O) HELIX 1 1 GLU A 9 MET A 32 1 24 HELIX 2 2 ASP A 36 LEU A 62 1 27 HELIX 3 3 TYR A 79 ASP A 102 1 24 HELIX 4 4 ASP A 104 THR A 128 1 25 HELIX 5 5 VAL A 130 GLY A 155 1 26 HELIX 6 6 VAL A 167 GLY A 192 1 26 HELIX 7 7 PRO A 200 VAL A 217 1 18 HELIX 8 8 VAL A 217 ARG A 225 1 9 HELIX 9 9 SER A 226 PHE A 230 5 5 SHEET 1 A 2 THR A 67 PHE A 71 0 SHEET 2 A 2 GLU A 74 ILE A 78 -1 O ILE A 78 N THR A 67 LINK NZ LYS A 216 C15 RET A 301 1555 1555 1.28 SITE 1 AC1 10 TRP A 86 THR A 90 LEU A 93 TRP A 138 SITE 2 AC1 10 SER A 141 TRP A 182 TYR A 185 ASP A 212 SITE 3 AC1 10 ALA A 215 LYS A 216 SITE 1 AC2 2 PHE A 135 LEU A 190 SITE 1 AC3 7 THR A 24 LEU A 28 ALA A 44 THR A 47 SITE 2 AC3 7 PHE A 54 ALA A 110 TYR A 147 SITE 1 AC4 4 LEU A 87 PRO A 91 LEU A 95 VAL A 112 CRYST1 60.745 60.745 108.240 90.00 90.00 120.00 P 63 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016462 0.009505 0.000000 0.00000 SCALE2 0.000000 0.019009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009239 0.00000